Abstract Blue whales were brought to the edge of extinction by commercial whaling in the twentieth century and their recovery rate in the Southern Hemisphere has been slow; they remain endangered. Blue whales, although the largest animals on Earth, are difficult to study in the Southern Hemisphere, thus their population structure, distribution and migration remain poorly known. Fortunately, blue whales produce powerful and stereotyped songs, which prove an effective clue for monitoring their different ‘acoustic populations.’ The DGD-Chagos song has been previously reported in the central Indian Ocean. A comparison of this song with the pygmy blue and Omura’s whale songs shows that the Chagos song are likely produced by a distinct previously unknown pygmy blue whale population. These songs are a large part of the underwater soundscape in the tropical Indian Ocean and have been so for nearly two decades. Seasonal differences in song detections among our six recording sites suggest that the Chagos whales migrate from the eastern to western central Indian Ocean, around the Chagos Archipelago, then further east, up to the north of Western Australia, and possibly further north, as far as Sri Lanka. The Indian Ocean holds a greater diversity of blue whale populations than thought previously.